During semiconductor substrate processing operations, solid residues of process chemistry tend to accumulate on the internal walls and surfaces of the reaction chamber. These residues can build up on the inside of the chamber and can dissolve, detach or otherwise disperse through the chamber during subsequent processing, resulting in substrate contamination and yield loss, or changes in chamber performance leading to a lack of wafer-to-wafer processing uniformity. Consequently, the residues that accumulate on the interior surfaces of the chamber are periodically removed. Removal chemistries must be both effective and compatible with the chamber materials in order not to damage chamber components. Organic residues may be cleaned with oxygen containing chemistries. However, silicon containing residues may require fluorine containing chemistries to clean. Certain chamber materials may be incompatible with certain chemistries. For example, quartz windows may be incompatible with fluorine containing chemistries.